A defect inspecting apparatus includes a reference image generator configured to generate a first reference image and a second reference image from design layout data. An image inspector is configured to obtain a first inspection image of a first inspection region of a photomask and a second inspection image of a second inspection region of the photomask. An operation processor is configured to extract a first coordinate offset by comparing the first inspection image with the first reference image and to extract a second coordinate offset by comparing the second inspection image with the second reference image.